qtasktimer
This is a simple timer for timeboxing, Pomodoro Technique, etc. that runs in systray. It's written in Python and uses PyQt5.
Installation
$ pip install qtasktimer
Usage
$ qtt
This will start the app and the icon will appear in systray. Left-click on it to start a 25 minute timer or right-click to open a menu with more options.
This is how it looks more or less in the middle of a pomodoro: